ArticleActa crystallographica. Section D, Structural biology2020
Local and global analysis of macromolecular atomic displacement parameters.
Article in Acta crystallographica. Section D, Structural biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Confidence-guided cryo-EM map optimisation with LocScale-2.0.Nature communications · 2026Article
- A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands.Acta crystallographica. Section D, Structural biology · 2025Article
- Structure-based discovery of first inhibitors targeting the helicase activity of human PIF1.Nucleic acids research · 2024Article
- How Do Gepotidacin and Zoliflodacin Stabilize DNA Cleavage Complexes with Bacterial Type IIA Topoisomerases? 1. Experimental Definition of Metal Binding Sites.International journal of molecular sciences · 2024Article
- Identifying and avoiding radiation damage in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2024Article
- Using graphlet degree vectors to predict atomic displacement parameters in protein structures.Acta crystallographica. Section D, Structural biology · 2023Article
- Reanalysis of a μ opioid receptor crystal structure reveals a covalent adduct with BU72.BMC biology · 2023Article
- Updated restraint dictionaries for carbohydrates in the pyranose form.Acta crystallographica. Section D, Structural biology · 2022Article
- Atomic model validation using the CCP-EM software suite.Acta crystallographica. Section D, Structural biology · 2022Article
- B-factor accuracy in protein crystal structures.Acta crystallographica. Section D, Structural biology · 2022Article
- A method for intuitively extracting macromolecular dynamics from structural disorder.Nature communications · 2021Article
- 'International journal of molecular sciences · 2021Article
- The missing link: covalent linkages in structural models.Acta crystallographica. Section D, Structural biology · 2021Article
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3 authors.
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Abstract
This paper describes the global and local analysis of atomic displacement parameters (ADPs) of macromolecules in X-ray crystallography. The distribution of ADPs is shown to follow the shifted inverse-gamma distribution or a mixture of these distributions. The mixture parameters are estimated using the expectation-maximization algorithm. In addition, a method for the resolution- and individual ADP-dependent local analysis of neighbouring atoms has been designed. This method facilitates the detection of mismodelled atoms, heavy-metal atoms and disordered and/or incorrectly modelled ligands. Both global and local analyses can be used to detect errors in atomic models, thus helping in the (re)building, refinement and validation of macromolecular structures. This method can also serve as an additional validation tool during PDB deposition.
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